Sunday, August 20, 2017

I still don't get area cladistics, and 'geographic paralogy' in particular

Since I started looking into panbiogeography and area cladistics, I have been curious about the concept of geographic paralogy. The word is used by area cladists (in the widest sense), and I have so far been doubtful about whether the analogy to gene paralogy fits.

To recap, area cladistics attempts to infer biogeographic area relationships from the patterns that species' areas of distribution show on a phylogenetic tree. If, for example, several plant or animal groups show distributions on a phylogeny that are ( Africa, ( South America , Australia ) ), i.e. sister lineages are endemic to South America and Australia, and more distantly related lineages are endemic to Africa, then an area cladist would conclude that South America and Australia are "more closely related" biogeographically than either is to Africa, or even that they form a "monophyletic biogeographic area".

Whatever that is supposed to mean, given that the word monophyletic only applies if we presuppose tree-like relationships. But I am getting ahead of myself.

The problem is now that phylogenies do not necessarily show such a simple pattern. Some species may be widespread and occur in several of the areas in the analysis, and of course the same area may occur repeatedly in different parts of the phylogeny. This is what area cladists call 'geographic paralogy', and they 'solve' the problem it poses for their analyses by selecting 'paralogy-free' subtrees from a phylogeny.

Again, two questions: Does it make sense to call this geographic paralogy, in analogy to gene paralogy? And does it make sense to do area cladistics by cherry-picking 'paralogy-free' subtrees, effectively ignoring these patterns?

I started a conversation with a colleague at the IBC, and he recommended I read Ladiges (1998, "Biogeography after Burbidge", Australian Systematic Botany 11: 231-242) as an introduction to the relevant concepts and approaches. So this I have now done. Unfortunately, the paper did not really solve my conceptual problems. I will start with a few quotes:
In cladistic biogeography, nodes of a cladogram for organisms (1,2 and 3) are potentially informative about the geographic areas (A, B and C) in which they occur: node 2 in Fig. 3 shows that areas B and C are related more closely to each other than to area A.

Such statements of relationship, the nodes of the cladogram, are explained by a variety of historical theories. One is dispersal from a restricted ancestral area, for example from area A to areas B and C, a pattern that may match fossil ages and distribution. An alternative explanation is vicariance of a widespread ancestral species coincident with physical breakup or climatic differentiation of the general area. A vicariance explanation is favoured by evidence of biogeographic congruence: finding the same pattern for other groups of organisms.
So far so good, although I do wonder whether the concept of area relationships makes sense if dispersal is the right answer. It seems to me that even calling it relationships only makes sense if there is no frequent floristic or faunal exchange, if near-everything is due to vicariance. And as I have mentioned before, there are good alternative explanations for congruence that do not imply vicariance, in particular prevailing directions of wind or ocean currents, common routes of migratory birds, etc.

Now come the complications:
Data for any one group of organisms are rarely as simple as the example shown (...). Some taxa are widespread, and some areas have more than one taxon. When combining data for different groups of organisms, not all areas are represented in each taxonomic group. Such complications are obstacles to development of analytical methods for determining area cladograms and general area cladograms.
Well yes, either that or, alternatively, they prove that the concept of an area cladogram is as incoherent as a 'species-level phylogeny' with only human populations as the terminals, and that the research program of area cladistics is a non-starter. Two pages on, the term at the centre of this post is introduced.
I offer two conclusions: (1) that evidence of historical geographic relationship is associated with nodes (not the distribution per se of terminal taxa) and (2) that some nodes of cladograms of organisms are paralogous. (...)

What is geographic paralogy? It is evidenced by duplication or overlap in geographic distribution of taxa related at a node (references). The term has its origin in molecular biology, geographic paralogy being analogous to gene duplication, with each gene copy subsequently tracking a separate evolutionary history.

(...) There is duplication of biogeographic regions across the clades (e.g. South America is in three), which is evidence of geographic paralogy. In other words, the major lineages shown in the cladogram existed prior to the breakup of Gondwana and each potentially reflects that geological history.
Consider what is claimed here. First, as we have seen earlier, simple area relationships that are congruent across lineages are claimed as evidence for vicariance. Now the fact that the same area shows up in several parts of a phylogeny is seen as evidence for paralogy; and this paralogy is also seen as evidence for vicariance and against dispersal. I cannot say that this makes a lot of sense to me.

Having gone through these quotes, I now want to carefully examine the analogy between gene paralogy and geographic paralogy. Let's start with the former. It works like this:



In this and the following figures, we see a grey species tree with species 1, 2 and 3. Within it we see the gene trees, as genes evolve inside the species. Here an originally single gene lineage (blue) was duplicated in the common ancestor of all three species, creating a red gene and a black gene. We now call the alleles A and Y paralogues of each other, because while they are distantly related they are not really the same gene anymore. In contrast, A and B are orthologues of each other. They are really the same gene, only in two different species.



The above figure now shows the problem that gene paralogy can cause in phylogeny reconstruction. If in this case Z is wrongly assumed to be an orthologue of A and B, we will infer the wrong species relationships, i.e. ((1,2),3) instead of the true (1,(2,3)). However, there are also other causes why we may get conflicting or complicated patterns.



In the above case we have the gene tree contradicting the species tree, but nonetheless there is no paralogy because there is only one gene involved. What has happened here is that two versions of the gene arose in an ancestral population, and that subsequent populations were large enough and/or speciation events happened so close after each other that both copies were carried through to the ancestor of 2 and 3. We call this incomplete lineage sorting (ILS) or ancestral polymorphism. We could also still find all gene variants in all three species. Point is, this is not paralogy.



Something different has happened in the above scenario. We get the same pattern of a gene tree showing ((1,2),3) despite the species phylogeny of (1,(2,3)), but this time because of a hybridisation or introgression event between 1 and 2. Of course, we could also still find the original gene variant in species 2 along with the introgressed one. Again, this is not paralogy.



Now the same for biogeography. Above the scenario where I think the analogy works: There are two clades that arose before continental breakup, and they both independently trace the 'area relationships'. In this case it makes sense to use the two clades or subtrees as independent data points for inference in area cladistics.



Here is the same problem for area cladistics as for phylogenetic inference. If we do not realise that we are treating paralogues as orthologues, we may get species phylogenies and, by analogy, area relationships wrong. So in the case of phylogenetics, people have developed methods for orthologue inference and to exclude paralogues from the data.

What I don't really see is how area cladists do the same. They claim they pick 'paralogue-free subtrees', but that merely means that they search for a statement like ((1,2),3) and remove statements like (1&2&3,(1&2,2&3)). It does  not mean that they actually have any way of recognising that ((1,2),3) is an instance of paralogy while (1,(2,3)) isn't. They can merely hope that it comes out in the wash because the true relationship will be more frequent than the wrong ones.

This appears to be rather problematic, unless I am missing something equivalent to orthology inference in phylogenetics. But on top of that we have the other scenarios, those where there really is no paralogy.



The above is the biogeographic equivalent of incomplete lineage sorting. We could imagine here that species C stayed endemic to a part of South America while its sister species was more widespread. If we now also had some species occurring in two areas, area cladists would speak of paralogous nodes, but again, there does not appear to be any paralogy involved.



But really crucial is the biogeographic parallel to gene introgression: dispersal. The above scenario shows what area cladists call paralogy and, as we saw in the quotes above, consider evidence of vicariance, but what reason is there to exclude dispersal as a possible explanation? This is, of course, precisely the pattern that dispersal would produce!

And it is clearly not in any way comparable to gene paralogy anyway, because there are no paralogues involved. It makes no sense to use a term that assumes the existence of two genes independently tracing the species phylogeny (and, by analogy, two species-lineages independently tracing 'area relationships') to refer to any difficult pattern, even where there are no such two deep species-lineages.

In summary, I am still not exactly convinced that area cladistics makes sense. The assumption that pretty much any pattern - congruence as well as the contradictory data from paralogy! - is evidence of vicariance seems particularly hard to swallow.

Tuesday, August 15, 2017

This is not how this works, religious freedom edition

Sometimes it is interesting what raises one's hackles. Today one could get upset about domestic terrorism in the USA or the level of discourse regarding dual citizenships in Australian politics, but what really annoyed me was an opinion piece on the ABC website with the title "same-sex marriage is more complex than the Yes campaign admits".

Basically, the author, one Peter Kurti identified as "a research fellow at the Centre for Independent Studies and the author of The Tyranny of Tolerance: Threats to Religious Liberty in Australia", argues that any changes to laws that will allow same-sex marriage will have to ensure that those who don't like that change can still discriminate against homosexuals:
Freedom of religion extends far beyond the walls of a church or a synagogue.

Schools, charities, and other faith-based not-for-profits, as well as ordinary business people such as bakers, florists, and photographers who wish to uphold the traditional meaning of marriage need to be protected from discrimination and attack if the law on marriage does change. [...]
   
If the law is eventually changed to allow same-sex couples to marry, it should not create an additional entitlement enabling some citizens to force other citizens to act against their religious beliefs or conscience by making them help celebrate same-sex marriages.
The usual disclaimer applies here as to how what I write is my private, non-professional opinion and not necessarily that of any other person or institution that I may be associated with, but I believe I am not stating anything particularly controversial or revolutionary when I now write:
This is not how freedom of religion works.

Let's consider how this would have to work in other cases, if it wasn't complete nonsense.
  • If the law is eventually changed to allow mixed-race couples to marry, it should not create an additional entitlement enabling some citizens to force other citizens to act against their religious beliefs or conscience by making them help celebrate mixed-race marriages.
  • If the law is eventually changed to allow women to seek employment, it should not create an additional entitlement enabling some citizens to force other citizens to act against their religious beliefs or conscience by making them hire women.
  • If the law is eventually changed to allow people to wear yellow shirts, it should not create an additional entitlement enabling some citizens to force other citizens to act against their religious beliefs or conscience by making them provide services to customers wearing yellow shirts.
The logic, and I am using this word loosely because any more appropriate alternative would be impolite, is exactly the same in all four cases. There is not one iota difference between them.

Freedom of religion, unless it is intended to destroy all personal freedom and tolerance, cannot mean that people get to discriminate against whatever they personally don't like. It means that they are allowed to follow their religious rules, for example by not marrying somebody of the same sex themselves, but it cannot mean that they are allowed to discriminate against others who do not follow those rules.

What really frustrates me is that this is not some random dude who has never looked into how rights and freedoms work and made some thoughtless off the cuff remark during lunch break. This is somebody who has carefully written an opinion piece and got it published by Australia's public broadcasting company on the strength of their authority as a scholar. I assume it would be silly to ask if the piece underwent peer review.

Monday, August 14, 2017

Botany picture #250: Aristolochia clematitis


Aristolochia clematitis (Aristolochiaceae), the only member of its genus in Germany, 2008. I rather like this genus with its weird flowers, but unfortunately I very rarely see them in the wild. It took me years before I ran into this one in Europe, and otherwise I have only seen the odd one or two species in South America. There are certainly none near where I live now.

Friday, August 11, 2017

Does philosophy produce knowledge?

Recently I jumped, rather rashly, into a discussion about the purpose of philosophy. On his blog, philosopher Daniel Kaufman commented on the suggestion by a different philosopher that philosophy PhD students should be banned from publishing and took the opportunity to argue that there were too many PhDs hunting too many jobs, partly because graduate students were exploited as cheap labour, everybody was publishing too much, many of the leading philosophers weren't doing enough undergraduate teaching, and the field had gone down a dangerous and misguided path by assuming that it was a knowledge-generating exercise like science.

In Kaufman's telling, (a) philosophy does not generate knowledge ("these are not the sorts of questions that will ever admit of conclusive answers") but its purpose is to enrich our lives, (b) universities should fund things that enrich our lives even when they do not generate knowledge, and (c) admitting that philosophy does not generate knowledge is the best strategy for minimising future funding cuts, while trying to play scientist will backfire.

I could clearly have expressed myself better, especially in my first comment, but my position is that (a) philosophy can generate knowledge, (b) I do not see why universities should teach things that are self-admittedly non-academic, and (c) I strongly doubt that pitching philosophy as intellectually futile is going to work in its favour.

Note that I am not saying in any way whatsoever that universities should only train people for jobs, quite the opposite. I am merely saying that they are there to produce, manage and transfer knowledge (e.g. history of music or theory of music), while mere amusement or practical skills (e.g. appreciating music or learning to play the piano) are better accommodated in other ways, for example by buying a music CD or paying a private piano teacher. I am also not saying that anything that doesn't produce, manage or transfer knowledge is useless, merely that such a non-academic activity could perhaps better be accommodated outside of the university.

The main point I want to discuss now is, however, the first: can philosophy produce knowledge? The example that I would like to use is that of divine command theory and the Euthyphro dilemma. It may be said that that is very low-hanging fruit, but well, if somebody wanted to show how science can produce knowledge they would also choose something simple like the shape of the earth as opposed to the minutiae of population genetics or quantum physics.

As most people will know, divine command theory is the claim that "what is moral is determined by what God commands, and that for a person to be moral is to follow his commands" (quoted from Wikipedia, 11 Aug 2017). As most people will also know, Plato challenged this idea with the Euthyphro dilemma, which in modern terms is perhaps best summarised as follows:

There are two possibilities. Either the gods command that some action is moral because it is moral by an independent, objective standard. If that is the case, then we can cut out the middleman and conclude that morality does not actually flow from the gods. Alternatively, whatever random thing the gods declare moral is moral merely because the gods say so. If that is how it works, what if the gods commanded you to torture an innocent person to death? Clearly the first option is incompatible with divine command theory, but if the alternative is accepted then the theory is shown to have absurd consequences.

Religious people have, of course, tried to find answers to this dilemma. They seem to fall mostly into two categories, either stating that god would never command something evil, which even if they do not realise it grants that there is an independent standard and thus divine command theory is false, or claiming that the answer is "both", that there is no dilemma. As I have written on this blog before, that latter rebuttal does not work because both you can't avoid a bad outcome by accepting two bad options. If a judge asks whether you have murdered your neighbour or whether you got him killed through recklessness replying "both, your honour" won't clear you either.

I would consequently argue that Plato's philosophy has in this case generated a piece of knowledge: divine command theory does not work. And it was generated through philosophy as opposed to science, as no empirical data were involved.

What possible objections could be raised?

First, this is merely what we might call 'negative' knowledge. We still don't know what to base our moral reasoning on, merely that we cannot base it on "but the gods said so". To this I would respond that there is a clear parallel in science, which can also test and reject hypotheses and models but only ever tentatively (!) keep the ones that are currently not superseded and rejected.

Second, it could be argued somebody could find a solution to the dilemma or perhaps already has found a solution to the dilemma. Again the parallel to science should be clear: knowledge is always tentative until somebody comes along and disproves it and/or suggests an even better idea. The fact that we are never omniscient does not mean that we are as ignorant after somebody has thought through a problem as we were before.

Third, it could be observed that there are still plenty of people working as philosophers who accept divine command theory. And once more I would like to point towards the example of science. There are plenty of creationists, even some (if few) biologists; does that mean that biology does not produce knowledge? The only difference is that even the professionals in philosophy share less consensus on what is right than professional biologists.

Here I would argue that how much of a consensus can be achieved in a field depends on two main factors: whether the knowledge produced by the field is important in some kind of practice, and whether there is a lot of motivation to continue accepting a falsehood. Engineering, for example, has immediate and crucial practical applications. If an engineer accepts nonsense, they may construct something that fails embarrassingly, and consequently engineers are very likely to reject nonsense in their field of expertise (this qualifier is obviously important).

Economists, on the other hand, work in a field where things do not just work or fail, but they generally work in favour of either this interest group or that interest group. Even if raising wages would be "better" for the economy as a whole, it might still not be in the interest of individual investors; and even if lowering wages would be "better" for the competitiveness of an economy, it might still not be in the interest of an individual employee who wants more money now. It therefore seems entirely unsurprising to me that there would be a lot of motivated reasoning in economics, making it hard to discard false beliefs.

Philosophy has no immediate applications on the lines of keeping a bridge up, but it certainly deals with a lot of questions that are dear to people or affect closely held beliefs, for example ethics or epistemology. It therefore seems entirely unsurprising to me that the field would have it harder to discard false beliefs than chemistry or geography, for example. The take-home message here is that individual practitioners disagreeing does not demonstrate that there is no knowledge to be had; it may merely indicate that some practitioners reject that knowledge due to personal biases.

In conclusion, I remain convinced that philosophy does, or at least can, generate knowledge. It does so, among other approaches, by thought experiment, showing claims to lead to absurd consequences, or showing claims to involve a self-contradiction. Much of that may be rejection as opposed to proving of claims, but again, science is also mostly rejection of false ideas. The (always tentative) understanding we have now is what remained after myriads of mistakes were corrected.

Wednesday, August 9, 2017

Discussions of diversity and equality are generally very depressing

Somebody at Google circulated an opinion piece on Google's diversity efforts, which was ultimately published by Gizmodo. A public discussion ensued. And as always with what is called "cultural" issues I find the way it goes very depressing. Perhaps surprisingly that is not because of some particularly backwards or intolerant position taken by this or that participant (although that too, see #6 below), but rather because much of what goes on in these kinds of discussions seems so futile.

One of the most fundamental problems is that there is not actually one controversy, there are numerous controversies going on at the same time, and people mix them all up. Just checking out two articles or posts and following their links to perhaps another three, it seems to me as if at least all of this is being discussed at the same time, in no particular order:

1. Whether there are psychological differences between men and women.

2. If such differences exist, to what degree they are genetic/developmental or socially conditioned.

3. Whether there are cognitive differences between men and women to the degree that the average man is objectively better at abstract problem solving and thus more suited for being a software engineer than the average woman.

4. Whether there are cognitive differences between men and women to the degree that the average man is objectively better at abstract problem solving than the average woman, but because software engineering is really a collaborative and thus people-oriented activity, at which women are said to excel, the average woman makes a better software engineer than the average man.

5. Whether different levels of representation of men and women in different fields of work are now largely due to job preferences as opposed to discrimination, meaning that trying to achieve parity in all fields is futile.

6. Whether women are, and I quote, "inferior" in sports. Yeah, I have no idea what that has to do with anything either, but I believe the choice of terminology speaks volumes.

7. Whether Google (and by extension many other companies) now has been captured by "the left" and has adopted "political correctness" to the degree that nobody dares to speak their mind for fear of being shamed, ostracised, and fired.

8. Whether Google was justified in firing the author of the memo for being disruptive and/or violating its code of conduct.

9. Whether circulating this memo to colleagues falls under the Free Speech guarantee of the US constitution.

And I am sure I have missed some. For what it is worth, the way I understand the original memo it was clumsily trying to argue mostly #5 and #7 and potentially #3, or at least it is widely read as arguing the latter.

In light of this it is unsurprising that so little is achieved and that so many people are at each others' throats. Of course there are many other topics where people will have heated discussions, but it is because their opinions differ very strongly (e.g. economic policy, environment, energy), not merely because they are completely talking past each other.

But with these equality / diversity issues I regularly see people go ballistic at each other who seem to pretty much agree on policy goals (e.g. better representation of currently underrepresented groups), general political outlook and acceptance of empirical reality (e.g. differences in mean innate cognitive abilities between groups of humans are negligible compared to variance within those groups) and should consequently be able to hash their differences out in a more rational manner.

One person says "maybe it is mostly job preferences now" but the other hears it as "I want to excuse under-payment and harassment of women"; or one person says "what he wrote could be read as if women don't make good engineers, and that creates a hostile work environment" and the other hears it as "nobody is allowed to have a different opinion than me; burn, heretic!" Makes me despair of political discourse.

Tuesday, August 8, 2017

Botany picture #249: Nothofagus of Patagonia


Deciduous Nothofagus (Fagaceae) trees near Puerto Blest, Argentina, in 2009. Or whatever the current genus name for this subgroup of southern beeches is after Nothofagus has been split up. In this case the reason for taxonomic changes was not phylogenetic systematics, because Nothofagus in its wider circumscription was also monophyletic. If I understand correctly, the idea was to make the age of the genera more comparable to Quercus, Fagus and suchlike. Either way, I like how this picture came out.

Sunday, August 6, 2017

Undergraduate resumes / CVs

I don't seem to have one of those files on my current computers any more, but I know that my CV as an undergraduate looked something like this:
Name
Address

Picture taken by professional photographer while I was wearing a formal jacket and perhaps a tie

Formation

Studying biology at [university], 1996 - now
Non-military service, 1995 - 1996
[Public grammar school] (high school & college in one), 1988 - 1997
[Yet another public school], 1986 - 1988
[Public primary school], 1982 - 1986

Undergraduate scholarship of [foundation], 1997 - now
And... that was that. Black on white, Times New Roman size 11 point, 1.2 line spacing, one page, easy to see all relevant information at a glance.

Now, an Australian undergraduate's CV today appears to look something like the following:
Name
Address, e-mail

Either no picture (which is what is expected in Australia) or a selfie taken at a party

Personal details

My name is [name], I am 24 years old and live in Woolalla, New South Wales. I am currently in my third year at Ned Kelly University studying a combined degree Bachelor of Science / Bachelor of Arts majoring in biology and journalism. I hope to pursue a career in science and apply what I learned in university to better the world.

Personal attributes

Effective communicator
Reliable and trustworthy
Ability to work in team as well as independently
Hard worker
Leadership skills demonstrated by frying burgers at McDonalds
Organisation talent demonstrated during waitressing by correctly taking customer's orders

Skills

Word, Excel, PowerPoint, Internet Explorer, Google

Employment history

Sales assistant at some supermarket, 2009 - now
Waitressing at Happy Hogan's bar, 2008-2012
Frying burgers at McDonalds, 2013 - now

Volunteer work and leadership

Friends of the State Zoo, 2011 - now
Church Youth, 2007 - 2009

Education

Ned Kelly University,  Bachelor of Science / Bachelor of Arts majoring in biology and journalism, 2014 - now
Catholic College of South-eastern Western North Sydney, 2012 - 2014
Little Sisters of Perpetual Misery Private Catholic High School, 2008 - 2012

Other activities

Raising money for YUZN charity
Wildlife rescue
Greening Australia
Surfing
Blood donor for Red Cross
Debate club

Achievements

Consistently excellent marks in university*
Award for high placement
Mentor for other students
Talent Award
Award for outstanding job as house head
President of debate club
Dean's letter of recommendation
They are often carefully formatted in a fancy sans serif font with about 50% white space, perhaps a red bar at the top or a blue bar along the left margin of the page. They are often three to four pages long.

A few thoughts. First, it is not as if we didn't have extracurricular activities and hobbies back then in Germany. It just would never have occurred to most of us that a potential employer or scholarship provider would care the least bit about our participation in a badminton club. And as far as I can tell they wouldn't have, and I certainly don't. This is wasted space that merely makes it harder to find the truly relevant information.

Second, the personal attributes also seem a bit pointless. Will anybody actually truthfully write "I am lazy" or "I am a poor communicator"? Presumably not, everybody will claim the positives, honestly or not. So this is wasted space that merely makes it harder to find the truly relevant information.

Third, I assume somebody tells Australian students to put all their work experience in there to demonstrate ... well, this is where it breaks down for me. That they will show up for work if you give them a contract? That's kind of a low hurdle to clear. But beyond that, how is flipping burgers or waiting tables a relevant qualification for a job or scholarship in science? I don't get it. This is wasted space that merely makes it harder to find the truly relevant information.

Fourth, all those achievements? When I was a school or university student in Germany, we did not have even just a tenth of those awards. Here half the students seem to have lists of awards that look seriously impressive; but given how many of them have lists like that I do wonder how easy they are to get. If there is no term like award inflation (in analogy to grade inflation) then we need to create it.

Of course, given the length of the time since I left I also wonder how German undergraduate students' CVs look these days. Do they now also mention every little thing they did, no matter how irrelevant to the job or scholarship they are applying for? Do they also now try to look as if they had been written by a graphic design graduate?

Footnote

*) From what I can tell the likelihood of somebody explicitly claiming to have consistently high marks in the achievement list seems negatively correlated with the actual quality of their marks. The people who actually have near-straight high distinctions tend to have only an understated line in the CV providing their point average.